FIMO is a software tool for scanning DNA or protein sequences for occurrences of motifs described by position-specific scoring matrices. It calculates a log-likelihood ratio score for each position in a sequence database, converts this score to a P-value using dynamic programming, and applies false discovery rate analysis to estimate a q-value for each position. FIMO provides output in various formats, including HTML, XML, and formats suitable for the UCSC Genome Browser. It is efficient, scanning DNA sequences at 3.5 Mb/s on a single CPU. FIMO is part of the MEME Suite and is available via a web server and source code. It is designed to identify individual candidate binding sites or protein motifs. FIMO is simpler and more general than other motif scanning algorithms like MAST and MCAST. It only assigns scores to individual motif occurrences, not to joint occurrences or sequence regions. FIMO takes as input fixed-length motifs represented as position-specific frequency matrices, which can be generated from the MEME algorithm or created manually. It computes log-likelihood ratio scores, converts them to P-values, and estimates false discovery rates. FIMO produces a ranked list of motif occurrences with associated scores, P-values, and q-values. It is used to identify candidate CTCF binding sites in the human genome, with results showing high precision for top-scoring occurrences. FIMO scanning the entire human genome took 30 minutes on an Intel Xeon CPU. Funding was provided by the National Institutes of Health. No conflicts of interest were declared.FIMO is a software tool for scanning DNA or protein sequences for occurrences of motifs described by position-specific scoring matrices. It calculates a log-likelihood ratio score for each position in a sequence database, converts this score to a P-value using dynamic programming, and applies false discovery rate analysis to estimate a q-value for each position. FIMO provides output in various formats, including HTML, XML, and formats suitable for the UCSC Genome Browser. It is efficient, scanning DNA sequences at 3.5 Mb/s on a single CPU. FIMO is part of the MEME Suite and is available via a web server and source code. It is designed to identify individual candidate binding sites or protein motifs. FIMO is simpler and more general than other motif scanning algorithms like MAST and MCAST. It only assigns scores to individual motif occurrences, not to joint occurrences or sequence regions. FIMO takes as input fixed-length motifs represented as position-specific frequency matrices, which can be generated from the MEME algorithm or created manually. It computes log-likelihood ratio scores, converts them to P-values, and estimates false discovery rates. FIMO produces a ranked list of motif occurrences with associated scores, P-values, and q-values. It is used to identify candidate CTCF binding sites in the human genome, with results showing high precision for top-scoring occurrences. FIMO scanning the entire human genome took 30 minutes on an Intel Xeon CPU. Funding was provided by the National Institutes of Health. No conflicts of interest were declared.